Some properties of the map set can be modified by using edit mapset command. As with the other objects, the map set can be specified by MapSetId or by path that includes the text from the map set tree parent nodes. The MapSetId of each map set is printed out by the command list mapset:

PS> list mapset
2: MSU_osa1r7                                               4: ASM465v1
10: GRCh38                                                  16: TAIR10
17: Sorghum v.3.1                                           18: BTx623-IS320C

In this listing, the highlighted value preceding the colon is the MapSetId.

To edit the map set specified by MapSetId run:

PS> edit mapset 16
Name? TAIR10
Accession? TAIR10
Description? Arabidopsis thaliana TAIR10 from  ftp://ftp.ensemblgenomes.org/pub/release-37/plants/genbank/arabidopsis_thaliana
quality ([0-4] or empty)? 4
Do you want to edit the mapset? (Y/N) Y
MapSet:16 has been successfully modified.

The map set can be specified by its full path in the map set tree. To save some typing, you can always use the auto-complete feature on the command line activated with the TAB key. The path should lead to the map set tree node:

PS> edit mapset "Arabidopsis thaliana/TAIR10"

Please look at quality property of the map set:

quality ([0-4] or empty)? 4

If set to a number between 0 and 4, the quality value will be shown in Persephone as a 'signal bars' icon, reflecting the quality of the map set (in the desktop version only, for now). If you want to show that a map set is in its early stage of sequencing, give it the lowest quality of 0. Mature genomes usually have the assembly quality of 4.

The quality value can be erased by entering an empty string. In this case the 'signal bars' icon will be hidden.

Edit multi-line description

The initial description is usually provided as a part of the INI file for loading a new map set. The description can contain multiple lines of text. If needed, it can later be modified by the command edit mapset. In case of a simple one-line description, the editing can be done in PersephoneShell by modifying the text displayed in one line. For complex cases, the multi-line text can be pasted from the clipboard. You can copy the existing text of the description to the clipboard from the screen, edit it in an external editor, and paste it back to PersephoneShell:


PS> edit mapset "Oryza sativa indica/ASM465v1"
Name? ASM465v1
Accession? ASM465v1
OrganismId? 39946
Description:
Oryza sativa indica. Cultivar 93-11. 
The genome assembly represented here corresponds to <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000004655.2/">GCA_000004655.2</a> masked genomic DNA. 

Just hit ESC to keep the old value of Description.
Ctrl-F - Read new text from file; Ctrl-T - Paste the new text from clipboard
Paste the new text from the clipboard. Add an empty line at the end and hit Ctrl-D
Oryza sativa indica. Cultivar 93-11.
The genome assembly represented here corresponds to <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000004655.2/">GCA_000004655.2</a> masked genomic DNA.

New Description:
Oryza sativa indica. Cultivar 93-11.
The genome assembly represented here corresponds to <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000004655.2/">GCA_000004655.2</a> masked genomic DNA.
Interspersed repeats and low complexity regions are detected with the RepeatMasker tool and masked by replacing repeats with 'N's.
The sequences were downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-37/fasta/oryza_indica/dna/Oryza_indica.ASM465v1.dna_sm.toplevel.fa.gz

Upon pasting the text, add an empty line and hit Ctrl-D to finish the entry.

Note

The description can contain HTML tags, such as <i>, <b> or <a>. When providing the hyper-links by pasting the text, you can use the quotation marks as they are, verbatim (see the example above). This is different from the format of the hyperlinks in the INI files: the multi-line values should be given in double quotes, so the internal quotation marks which are required by the <a> tag should be escaped by the backslash:
Click this <a href=\"http://link\"> URL label </a>

Edit map set using a control file

In case there is the need to edit multiple map sets and modify the same values, such as the flag IsActive or OrganismId, use the command line version that uses the control file.

PS> edit mapset 2 -c setactive.ini

To apply the edits to multiple map sets, use a script with different map sets on each command line of the OS terminal and use the command line mode of PersephoneShell:

$psh edit mapset 2 -c setactive.ini
$psh edit mapset 3 -c setactive.ini
$psh edit mapset 4 -c setactive.ini

A sample control file is shown below:

[MapSet]
;Name=new name
;Accession=new accession
;OrganismId=new ID
;Description="multi line
;description"
IsActive=true

[Qualifiers]
;quality=4
;Technology=T2T

The control file allows changing the map set Name, Accession, OrganismId, Description, the IsActive flag, plus, adding or modifying map set qualifiers.